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PDBsum entry 1gpm

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protein ligands metals Protein-protein interface(s) links
Transferase (glutamine amidotransferase) PDB id
1gpm
Jmol
Contents
Protein chains
501 a.a. *
Ligands
PO4 ×4
POP ×4
AMP ×4
CIT ×4
Metals
_MG ×3
Waters ×790
* Residue conservation analysis
PDB id:
1gpm
Name: Transferase (glutamine amidotransferase)
Title: Escherichia coli gmp synthetase complexed with amp and pyrop
Structure: Gmp synthetase. Chain: a, b, c, d. Synonym: xmp aminase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: guaa. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: tac promoter
Biol. unit: Tetramer (from PQS)
Resolution:
2.20Å     R-factor:   0.174    
Authors: J.J.G.Tesmer
Key ref: J.J.Tesmer et al. (1996). The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nat Struct Biol, 3, 74-86. PubMed id: 8548458
Date:
04-Apr-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04079  (GUAA_ECOLI) -  GMP synthase [glutamine-hydrolyzing]
Seq:
Struc:
 
Seq:
Struc:
525 a.a.
501 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.5.2  - Gmp synthase (glutamine-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
AMP and GMP Biosynthesis
      Reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate
ATP
+ XMP
+ L-glutamine
+ H(2)O
=
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
+
diphosphate
Bound ligand (Het Group name = POP)
corresponds exactly
+ GMP
+
L-glutamate
Bound ligand (Het Group name = CIT)
matches with 64.29% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     glutamine metabolic process   3 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
Nat Struct Biol 3:74-86 (1996)
PubMed id: 8548458  
 
 
The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.
J.J.Tesmer, T.J.Klem, M.L.Deras, V.J.Davisson, J.L.Smith.
 
  ABSTRACT  
 
The crystal structure of GMP synthetase serves as a prototype for two families of metabolic enzymes. The Class I glutamine amidotransferase domain of GMP synthetase is found in related enzymes of the purine, pyrimidine, tryptophan, arginine, histidine and folic acid biosynthetic pathways. This domain includes a conserved Cys-His-Glu triad and is representative of a new family of enzymes that use a catalytic triad for enzymatic hydrolysis. The structure and conserved sequence fingerprint of the nucleotide-binding site in a second domain of GMP synthetase are common to a family of ATP pyrophosphatases, including NAD synthetase, asparagine synthetase and argininosuccinate synthetase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19834552 F.Sarkari, T.Sanchez-Alcaraz, S.Wang, M.N.Holowaty, Y.Sheng, and L.Frappier (2009).
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Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
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PDB code: 3dla
18294973 D.Iwata-Reuyl (2008).
An embarrassment of riches: the enzymology of RNA modification.
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18458150 E.J.Hart, and S.G.Powers-Lee (2008).
Mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad?
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18668122 Y.Ikeuchi, K.Kitahara, and T.Suzuki (2008).
The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon.
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17269935 E.L.Ang, J.P.Obbard, and H.Zhao (2007).
Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis.
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17512708 M.J.Wagemaker, D.C.Eastwood, C.van der Drift, M.S.Jetten, K.Burton, L.J.Van Griensven, and H.J.Op den Camp (2007).
Argininosuccinate synthetase and argininosuccinate lyase: two ornithine cycle enzymes from Agaricus bisporus.
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18073113 M.Kuratani, Y.Yoshikawa, Y.Bessho, K.Higashijima, T.Ishii, R.Shibata, S.Takahashi, K.Yutani, and S.Yokoyama (2007).
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
  Structure, 15, 1642-1653.
PDB codes: 2e21 2e89
17961828 R.Rodriguez-Suarez, D.Xu, K.Veillette, J.Davison, S.Sillaots, S.Kauffman, W.Hu, J.Bowman, N.Martel, S.Trosok, H.Wang, L.Zhang, L.Y.Huang, Y.Li, F.Rahkhoodaee, T.Ransom, D.Gauvin, C.Douglas, P.Youngman, J.Becker, B.Jiang, and T.Roemer (2007).
Mechanism-of-action determination of GMP synthase inhibitors and target validation in Candida albicans and Aspergillus fumigatus.
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17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
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17010373 J.Chartron, K.S.Carroll, C.Shiau, H.Gao, J.A.Leary, C.R.Bertozzi, and C.D.Stout (2006).
Substrate recognition, protein dynamics, and iron-sulfur cluster in Pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.
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PDB code: 2goy
16387658 J.D.Mougous, D.H.Lee, S.C.Hubbard, M.W.Schelle, D.J.Vocadlo, J.M.Berger, and C.R.Bertozzi (2006).
Molecular basis for G protein control of the prokaryotic ATP sulfurylase.
  Mol Cell, 21, 109-122.
PDB code: 1zun
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The effects of removing the GAT domain from E. coli GMP synthetase.
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PDB code: 2abw
16756505 N.G.Richards, and M.S.Kilberg (2006).
Asparagine synthetase chemotherapy.
  Annu Rev Biochem, 75, 629-654.  
16547008 N.Shigi, Y.Sakaguchi, T.Suzuki, and K.Watanabe (2006).
Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures.
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16871210 T.Numata, Y.Ikeuchi, S.Fukai, T.Suzuki, and O.Nureki (2006).
Snapshots of tRNA sulphuration via an adenylated intermediate.
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PDB codes: 2der 2det 2deu
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PDB code: 1znn
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Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.
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PDB code: 1wy5
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PDB codes: 1uwd 1wcj
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Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases.
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15849257 R.E.Amaro, R.S.Myers, V.J.Davisson, and Z.A.Luthey-Schulten (2005).
Structural elements in IGP synthase exclude water to optimize ammonia transfer.
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16039592 Y.Ikeuchi, A.Soma, T.Ote, J.Kato, Y.Sekine, and T.Suzuki (2005).
molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition.
  Mol Cell, 19, 235-246.  
15805504 Y.Mitani, X.Meng, Y.Kamagata, and T.Tamura (2005).
Characterization of LtsA from Rhodococcus erythropolis, an enzyme with glutamine amidotransferase activity.
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15511226 F.A.Lunn, and S.L.Bearne (2004).
Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel.
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14585832 J.A.Bauer, E.M.Bennett, T.P.Begley, and S.E.Ealick (2004).
Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis.
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PDB code: 1r9g
15157079 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2004).
Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets.
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PDB code: 1s1m
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The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: a member of the DJ-1/ThiJ/PfpI superfamily.
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PDB codes: 1rw7 4qyx
15296735 M.Goto, R.Omi, N.Nakagawa, I.Miyahara, and K.Hirotsu (2004).
Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites.
  Structure, 12, 1413-1423.
PDB codes: 1vcm 1vcn 1vco
14527414 A.Soma, Y.Ikeuchi, S.Kanemasa, K.Kobayashi, N.Ogasawara, T.Ote, J.Kato, K.Watanabe, Y.Sekine, and T.Suzuki (2003).
An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.
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14506286 D.E.Pilloff, and T.S.Leyh (2003).
Allosteric and catalytic functions of the PPi-binding motif in the ATP sulfurylase-GTPase system.
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12752439 D.Simard, K.A.Hewitt, F.Lunn, A.Iyengar, and S.L.Bearne (2003).
Limited proteolysis of Escherichia coli cytidine 5'-triphosphate synthase. Identification of residues required for CTP formation and GTP-dependent activation of glutamine hydrolysis.
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12833548 K.Cox, T.Watson, P.Soultanas, and J.D.Hirst (2003).
Molecular dynamics simulations of a helicase.
  Proteins, 52, 254-262.  
12796482 K.Honbou, N.N.Suzuki, M.Horiuchi, T.Niki, T.Taira, H.Ariga, and F.Inagaki (2003).
The crystal structure of DJ-1, a protein related to male fertility and Parkinson's disease.
  J Biol Chem, 278, 31380-31384.
PDB code: 1ucf
12684518 M.Goto, R.Omi, I.Miyahara, M.Sugahara, and K.Hirotsu (2003).
Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.
  J Biol Chem, 278, 22964-22971.
PDB codes: 1j1z 1j20 1j21 1kh3
12547821 N.Hara, K.Yamada, M.Terashima, H.Osago, M.Shimoyama, and M.Tsuchiya (2003).
Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
  J Biol Chem, 278, 10914-10921.  
12621151 P.M.Quigley, K.Korotkov, F.Baneyx, and W.G.Hol (2003).
The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad.
  Proc Natl Acad Sci U S A, 100, 3137-3142.
PDB code: 1n57
12799468 R.Amaro, E.Tajkhorshid, and Z.Luthey-Schulten (2003).
Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.
  Proc Natl Acad Sci U S A, 100, 7599-7604.  
11839304 A.Douangamath, M.Walker, S.Beismann-Driemeyer, M.C.Vega-Fernandez, R.Sterner, and M.Wilmanns (2002).
Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex.
  Structure, 10, 185-193.
PDB codes: 1gpw 1k9v
11756425 A.Saeed-Kothe, and S.G.Powers-Lee (2002).
Specificity determining residues in ammonia- and glutamine-dependent carbamoyl phosphate synthetases.
  J Biol Chem, 277, 7231-7238.  
11809762 C.T.Lemke, and P.L.Howell (2002).
Substrate induced conformational changes in argininosuccinate synthetase.
  J Biol Chem, 277, 13074-13081.
PDB codes: 1kp2 1kp3
11953431 H.Li, T.J.Ryan, K.J.Chave, and P.Van Roey (2002).
Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate.
  J Biol Chem, 277, 24522-24529.
PDB code: 1l9x
12130656 J.B.Thoden, X.Huang, F.M.Raushel, and H.M.Holden (2002).
Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia.
  J Biol Chem, 277, 39722-39727.
PDB code: 1m6v
12012333 L.Aravind, V.Anantharaman, and E.V.Koonin (2002).
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.
  Proteins, 48, 1.  
11844799 M.Goto, Y.Nakajima, and K.Hirotsu (2002).
Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action.
  J Biol Chem, 277, 15890-15896.
PDB codes: 1kh1 1kh2 1kor
12360532 S.Korolev, T.Skarina, E.Evdokimova, S.Beasley, A.Edwards, A.Joachimiak, and A.Savchenko (2002).
Crystal structure of glutamine amidotransferase from Thermotoga maritima.
  Proteins, 49, 420-422.
PDB code: 1kxj
11371633 G.Spraggon, C.Kim, X.Nguyen-Huu, M.C.Yee, C.Yanofsky, and S.E.Mills (2001).
The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.
  Proc Natl Acad Sci U S A, 98, 6021-6026.
PDB codes: 1i7q 1i7s
  11380987 H.C.Pace, and C.Brenner (2001).
The nitrilase superfamily: classification, structure and function.
  Genome Biol, 2, REVIEWS0001.  
11119647 M.M.Horvath, and N.V.Grishin (2001).
The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily.
  Proteins, 42, 230-236.  
11553770 M.T.Hilgers, and M.L.Ludwig (2001).
Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
  Proc Natl Acad Sci U S A, 98, 11169-11174.
PDB code: 1ie0
11160884 N.V.Grishin (2001).
KH domain: one motif, two folds.
  Nucleic Acids Res, 29, 638-643.  
11208798 T.J.Klem, Y.Chen, and V.J.Davisson (2001).
Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase.
  J Bacteriol, 183, 989-996.  
11395405 X.Huang, H.M.Holden, and F.M.Raushel (2001).
Channeling of substrates and intermediates in enzyme-catalyzed reactions.
  Annu Rev Biochem, 70, 149-180.  
10850988 A.K.Bera, S.Chen, J.L.Smith, and H.Zalkin (2000).
Temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile.
  J Bacteriol, 182, 3734-3739.  
11080634 C.E.Stevenson, F.Sargent, G.Buchanan, T.Palmer, and D.M.Lawson (2000).
Crystal structure of the molybdenum cofactor biosynthesis protein MobA from Escherichia coli at near-atomic resolution.
  Structure, 8, 1115-1125.
PDB code: 1e5k
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
10852731 M.A.Rishavy, W.W.Cleland, and C.J.Lusty (2000).
15N isotope effects in glutamine hydrolysis catalyzed by carbamyl phosphate synthetase: evidence for a tetrahedral intermediate in the mechanism.
  Biochemistry, 39, 7309-7315.  
10966576 M.Y.Galperin, and N.V.Grishin (2000).
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
  Proteins, 41, 238-247.  
10722656 P.M.Palenchar, C.J.Buck, H.Cheng, T.J.Larson, and E.G.Mueller (2000).
Evidence that ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis, may be a sulfurtransferase that proceeds through a persulfide intermediate.
  J Biol Chem, 275, 8283-8286.  
11114201 X.Du, I.G.Choi, R.Kim, W.Wang, J.Jancarik, H.Yokota, and S.H.Kim (2000).
Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution.
  Proc Natl Acad Sci U S A, 97, 14079-14084.
PDB code: 1g2i
  10338021 B.Zhang, L.Rychlewski, K.Paw┼éowski, J.S.Fetrow, J.Skolnick, and A.Godzik (1999).
From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions.
  Protein Sci, 8, 1104-1115.  
10508782 C.H.Weber, Y.S.Park, S.Sanker, C.Kent, and M.L.Ludwig (1999).
A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
  Structure, 7, 1113-1124.
PDB code: 1coz
  10595545 E.G.Mueller, and P.M.Palenchar (1999).
Using genomic information to investigate the function of ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis.
  Protein Sci, 8, 2424-2427.  
10387030 F.M.Raushel, J.B.Thoden, and H.M.Holden (1999).
The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia.
  Biochemistry, 38, 7891-7899.  
10587438 J.B.Thoden, X.Huang, F.M.Raushel, and H.M.Holden (1999).
The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.
  Biochemistry, 38, 16158-16166.
PDB codes: 1c30 1c3o 1cs0
10449718 T.Knöchel, A.Ivens, G.Hester, A.Gonzalez, R.Bauerle, M.Wilmanns, K.Kirschner, and J.N.Jansonius (1999).
The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications.
  Proc Natl Acad Sci U S A, 96, 9479-9484.
PDB code: 1qdl
10587437 T.M.Larsen, S.K.Boehlein, S.M.Schuster, N.G.Richards, J.B.Thoden, H.M.Holden, and I.Rayment (1999).
Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
  Biochemistry, 38, 16146-16157.
PDB code: 1ct9
9858783 A.Hewagama, H.I.Guy, M.Chaparian, and D.R.Evans (1998).
The function of Glu338 in the catalytic triad of the carbamoyl phosphate synthetase amidotransferase domain.
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9818189 F.M.Raushel, J.B.Thoden, G.D.Reinhart, and H.M.Holden (1998).
Carbamoyl phosphate synthetase: a crooked path from substrates to products.
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Carbamoyl phosphate synthetase: a tunnel runs through it.
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Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
  Biochemistry, 37, 8825-8831.
PDB code: 1a9x
9914248 J.L.Smith (1998).
Glutamine PRPP amidotransferase: snapshots of an enzyme in action.
  Curr Opin Struct Biol, 8, 686-694.  
9687376 J.L.Smith, and A.Thompson (1998).
Reactivity of selenomethionine--dents in the magic bullet?
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9753692 M.Rizzi, M.Bolognesi, and A.Coda (1998).
A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure.
  Structure, 6, 1129-1140.
PDB code: 2nsy
  9620974 R.Cantoni, M.Branzoni, M.Labò, M.Rizzi, and G.Riccardi (1998).
The MTCY428.08 gene of Mycobacterium tuberculosis codes for NAD+ synthetase.
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Singular points of protein beta-sheets.
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Crystal structure of phosphoadenylyl sulphate (PAPS) reductase: a new family of adenine nucleotide alpha hydrolases.
  Structure, 5, 895-906.
PDB code: 1sur
9174345 J.B.Thoden, H.M.Holden, G.Wesenberg, F.M.Raushel, and I.Rayment (1997).
Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product.
  Biochemistry, 36, 6305-6316.  
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Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
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The conformation of inosine 5'-monophosphate (IMP) bound to IMP dehydrogenase determined by transferred nuclear overhauser effect spectroscopy.
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Structure and function of the glutamine phosphoribosylpyrophosphate amidotransferase glutamine site and communication with the phosphoribosylpyrophosphate site.
  J Biol Chem, 271, 15549-15557.
PDB code: 1ecg
8805567 M.N.Isupov, G.Obmolova, S.Butterworth, M.A.Badet-Denisot, B.Badet, I.Polikarpov, J.A.Littlechild, and A.Teplyakov (1996).
Substrate binding is required for assembly of the active conformation of the catalytic site in Ntn amidotransferases: evidence from the 1.8 A crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase.
  Structure, 4, 801-810.
PDB codes: 1gdo 1gms 1xff 1xfg
  8895556 M.Rizzi, C.Nessi, A.Mattevi, A.Coda, M.Bolognesi, and A.Galizzi (1996).
Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis.
  EMBO J, 15, 5125-5134.
PDB code: 1nsy
8916230 M.Rizzi, C.Nessi, M.Bolognesi, A.Coda, and A.Galizzi (1996).
Crystallization of NAD+ synthetase from Bacillus subtilis.
  Proteins, 26, 236-238.  
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